Dbgap Tools#

Configuration File: dbgap_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the dbgap_tools.json configuration file.

Available Tools#

DbGaP_get_study (Type: DbGaPTool)#

Retrieve one dbGaP study’s full public metadata by its phs accession: description, medical condit…

DbGaP_get_study tool specification

Tool Information:

  • Name: DbGaP_get_study

  • Type: DbGaPTool

  • Description: Retrieve one dbGaP study’s full public metadata by its phs accession: description, medical conditions studied, release date, and phenotype/molecular dataset and variable counts. Example: phs_id=’phs000681’ returns the Diabetes Prevention Program Genetics study with 4 phenotype datasets and 15 variables. Metadata only – the underlying genotype/phenotype data requires Data Access Committee approval. Use DbGaP_search_studies to find a phs_id.

Parameters:

  • phs_id (string) (required) dbGaP study accession, e.g. ‘phs000681’.

Example Usage:

query = {
    "name": "DbGaP_get_study",
    "arguments": {
        "phs_id": "example_value"
    }
}
result = tu.run(query)

DbGaP_search_studies (Type: DbGaPTool)#

Search dbGaP (NCBI’s controlled-access US genotype-phenotype archive, the American counterpart to…

DbGaP_search_studies tool specification

Tool Information:

  • Name: DbGaP_search_studies

  • Type: DbGaPTool

  • Description: Search dbGaP (NCBI’s controlled-access US genotype-phenotype archive, the American counterpart to EGA) for studies by title keyword, via its FHIR API. Example: query=’diabetes’ returns the Diabetes Prevention Program Genetics study. Returns each study’s phs_id for use with DbGaP_get_study.

Parameters:

  • query (string) (required) Study title keyword, e.g. ‘diabetes’, ‘autism’.

  • limit ([‘integer’, ‘null’]) (optional) Max studies to return, 1-100. Default 25.

Example Usage:

query = {
    "name": "DbGaP_search_studies",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)